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Genomic methylation patterns in archaeological barley show de-methylation as a time-dependent diagenetic process

Smith, Oliver, Clapham, Alan J., Rose, Pam, Liu, Yuan, Wang, Jun, Allaby, Robin G.·2014·Scientific Reports
DOI 10.1038/srep05559PMC PMC4081896
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Abstract

Genomic methylation is variable under biotic and abiotic stresses in plants. In particular, viral infection is thought to significantly increase genomic methylation with particularly high activity around transposable elements. Here we present the genomic methylation profiles of grains of archaeological barley (Hordeum vulgare) from several strata from a site in southern Egypt, from the Napatan to the Islamic periods (800 BCE – 1812 CE). One sample tested positive for viral infection and exhibits an unusually high degree of genomic methylation compared to the rest. A decreasing trend in global methylation levels according to deposition date shows in-situ de-methylation of 5-methylcytosine, which can be described as a diagenetic process. This is most likely a deamination mediated de-methylation process and is expected to lead to 5 mC > T base modifications in addition to the C > U modifications due to cytosine deamination, so represents a time-dependent process of DNA diagenesis in ancient DNA.

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  • Immunoprecipitation is likewise extremely limited in practice due to the fast postmortem decay of CpG dinucleotides and DNA fragmentation, which reduce the number of potential DNA methylation targets available per fragment.

    “Immunoprecipitation is likewise extremely limited in practice due to the fast postmortem decay of CpG dinucleotides 167 and DNA fragmentation 62 , which reduce the number of potential DNA methylation targets available per fragment.”

    From Ancient DNA analysis (2021) · cites this paper as [167]

    The Results section (page unavailable) says fragmented DNA molecules carry fewer methylated cytosines, supporting the part of the sentence linked to this citation. It does not establish that immunoprecipitation is extremely limited in practice; the authors say their bead-based enrichment method does not appear to discriminate against smaller fragments. The separate citation attached to CpG decay is outside this verdict. (LLM, conf=0.86)

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Research works printed but not linked: 31

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Metadata

Authors
Smith, O., Clapham, A. J., Rose, P., Liu, Y., Wang, J., & Allaby, R. G.
Venue
Scientific Reports
Publisher
Springer Science and Business Media LLC
Published
2014-07-04
Volume
4
Issue
1
ISSN
2045-2322
DOI
10.1038/srep05559
PMC
PMC4081896
Cited by
59
References
2
Language
en
Licence

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